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AllonKleinLab / SPRING

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How to transform my expression matrix #5

Open QiangShiPKU opened 6 years ago

QiangShiPKU commented 6 years ago

Hello, I noticed the expression matrix in example_inputs is .npy and .p format. However, my expression matrix is matrix.mtx, barcodes.tsv, and genes.tsv from 10X genomics or matrix.txt with row names (genes) and column names (cells). How could I tranform these format to .npy and .p?

calebweinreb commented 6 years ago

Hi,

It is best to use the new version of SPRING which is available at https://github.com/AllonKleinLab/SPRING_dev.

We have an ipython notebook for beginning with 10X data files. Sam do you mind sending this?

On Sat, Aug 11, 2018 at 10:44 PM, Qiang notifications@github.com wrote:

Hello, I noticed the expression matrix in example_inputs is .npy and .p format. However, my expression matrix is matrix.mtx, barcodes.tsv, and genes.tsv from 10X genomics or matrix.txt with row names (genes) and column names (cells). How could I tranform these format to .npy and .p?

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swolock commented 6 years ago

You should be able follow this example jupyter notebook to build a (new version) SPRING plot from your 10X data. Let us know if you run into any issues.

QiangShiPKU commented 6 years ago

Thanks，I will try